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Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault
ENRICHR_FORMATNoOutput format: detailed, compact, or minimaldetailed
ENRICHR_LIBRARIESNoComma-separated list of Enrichr libraries to querypop
ENRICHR_MAX_TERMSNoMaximum number of terms to show per library50
ENRICHR_OUTPUT_FILENoPath to save complete results as TSV file

Capabilities

Features and capabilities supported by this server

CapabilityDetails
tools
{
  "listChanged": true
}
prompts
{
  "listChanged": true
}
resources
{
  "listChanged": true
}
completions
{}

Tools

Functions exposed to the LLM to take actions

NameDescription
enrichr_analysis

Perform gene set enrichment analysis using Enrichr across multiple gene set libraries. Returns only statistically significant terms (adjusted p < 0.05).

Configured default libraries:

  • GO_Biological_Process_2026: Current Gene Ontology biological process terms — biological objectives and programs accomplished by gene products. The default choice for GO biological process enrichment.

  • KEGG_2026: Current KEGG metabolic and signaling pathways — the up-to-date KEGG release; prefer over older KEGG vintages.

  • Reactome_Pathways_2024: Current Reactome release — curated, peer-reviewed pathways for signaling, metabolism, gene expression, and disease.

  • MSigDB_Hallmark_2020: Hallmark gene sets representing well-defined biological states and processes from MSigDB.

  • ChEA_2022: ChIP-seq experiments from GEO, ENCODE, and publications identifying transcription factor-gene interactions from human and mouse.

  • GWAS_Catalog_2025: Current genome-wide association study results from the NHGRI-EBI GWAS Catalog, linking genes to human traits and diseases.

  • Human_Phenotype_Ontology: Standardized vocabulary of phenotypic abnormalities associated with human diseases.

  • PPI_Hub_Proteins: Highly connected hub proteins from protein-protein interaction networks.

  • DGIdb_Drug_Targets_2024: Drug-gene interactions from the Drug Gene Interaction Database — druggable targets and their compounds.

  • CellMarker_2024: Manually curated cell type markers from CellMarker database for human and mouse.

Any library in Enrichr's live catalog is accepted. Enrichr adds and retires libraries continuously, so do not rely on a memorized list: call suggest_libraries, or read the enrichr://libraries resource, to discover the libraries that currently exist.

Pass 'background' to test against a custom background gene set (for example, only the genes expressed in your assay) instead of Enrichr's whole-genome default. This is the statistically correct choice whenever the gene list was drawn from a restricted universe, and it matters: the whole-genome default can overstate significance by many orders of magnitude.

Each library's result reports 'backgroundCorrected'. If Enrichr's background service is unavailable the result falls back to uncorrected whole-genome p-values, flagged with a warning — treat those numbers as inflated and re-run rather than reporting them as background-corrected.

suggest_librariesA

Suggest relevant Enrichr libraries for a research question. Use this before enrichr_analysis to pick the best libraries for a specific topic.

Prompts

Interactive templates invoked by user choice

NameDescription
enrichment_analysisGuided workflow for gene set enrichment analysis with library selection and interpretation

Resources

Contextual data attached and managed by the client

NameDescription
library_catalogAll available Enrichr libraries organized by category
transcription librariesLibraries for a specific category
pathways librariesLibraries for a specific category
ontologies librariesLibraries for a specific category
diseases_drugs librariesLibraries for a specific category
cell_types librariesLibraries for a specific category
microRNAs librariesLibraries for a specific category
epigenetics librariesLibraries for a specific category
kinases librariesLibraries for a specific category
gene_perturbations librariesLibraries for a specific category
metabolomics librariesLibraries for a specific category
aging librariesLibraries for a specific category
protein_families librariesLibraries for a specific category
computational librariesLibraries for a specific category
literature librariesLibraries for a specific category
cancer librariesLibraries for a specific category
single_cell librariesLibraries for a specific category
chromosome librariesLibraries for a specific category
protein_interactions librariesLibraries for a specific category
structural librariesLibraries for a specific category
immunology librariesLibraries for a specific category
development librariesLibraries for a specific category
other librariesLibraries for a specific category

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